Atomistry » Sodium » PDB 3icf-3ivu » 3isd
Atomistry »
  Sodium »
    PDB 3icf-3ivu »
      3isd »

Sodium in PDB 3isd: Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch

Enzymatic activity of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd was solved by W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.19 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.700, 77.640, 55.220, 90.00, 113.67, 90.00
R / Rfree (%) 19.5 / 26.2

Other elements in 3isd:

The structure of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch (pdb code 3isd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch, PDB code: 3isd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3isd

Go back to Sodium Binding Sites List in 3isd
Sodium binding site 1 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:22.1
occ:1.00
O A:THR101 2.1 18.2 1.0
O A:ILE106 2.6 15.2 1.0
O A:VAL103 2.6 18.0 1.0
O A:HOH377 2.6 29.1 1.0
O P:HOH36 2.6 28.5 1.0
OP1 P:DG9 2.6 19.9 1.0
C A:THR101 3.1 16.4 1.0
C A:VAL103 3.4 19.1 1.0
P P:DG9 3.6 17.5 1.0
C A:ILE106 3.6 17.6 1.0
O A:HOH494 3.7 27.6 1.0
OP2 P:DG9 3.7 13.7 1.0
CA A:THR101 3.7 15.9 1.0
CA A:SER104 3.9 20.2 1.0
N A:SER104 4.0 19.7 1.0
N A:VAL103 4.0 19.1 1.0
N A:ILE106 4.0 17.3 1.0
N A:ARG102 4.2 16.1 1.0
C A:ARG102 4.2 18.3 1.0
N A:GLY105 4.2 18.7 1.0
CB A:THR101 4.3 14.3 1.0
CA A:ILE106 4.3 17.4 1.0
CA A:VAL103 4.4 19.2 1.0
C A:SER104 4.5 20.5 1.0
CA A:ARG102 4.5 17.2 1.0
O5' P:DG9 4.5 22.3 1.0
N A:GLY107 4.6 16.7 1.0
O A:LEU100 4.6 13.3 1.0
O A:ARG102 4.7 20.8 1.0
CB A:ILE106 4.8 16.2 1.0
CA A:GLY107 4.8 17.5 1.0
O3' P:DC8 4.8 19.9 1.0
N A:THR101 5.0 14.8 1.0

Sodium binding site 2 out of 3 in 3isd

Go back to Sodium Binding Sites List in 3isd
Sodium binding site 2 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:31.2
occ:1.00
O A:LEU62 2.0 24.6 1.0
O A:LYS60 2.4 19.1 1.0
OP1 D:DC3 2.6 20.6 1.0
O D:HOH6 2.7 25.5 1.0
C A:LEU62 2.8 24.9 1.0
O A:VAL65 3.0 23.6 1.0
C A:LYS60 3.5 21.5 1.0
N A:PRO63 3.5 25.7 1.0
N A:LEU62 3.5 25.1 1.0
C A:LYS61 3.6 25.1 1.0
CA A:LEU62 3.7 24.2 1.0
O A:LYS61 3.7 25.5 1.0
CA A:PRO63 3.7 25.2 1.0
C A:VAL65 3.9 23.0 1.0
P D:DC3 3.9 18.8 1.0
N A:VAL65 4.1 23.6 1.0
N A:GLY64 4.2 26.5 1.0
N A:LYS61 4.3 23.8 1.0
CA A:LYS61 4.3 24.9 1.0
C A:PRO63 4.4 26.3 1.0
CA A:LYS60 4.4 20.7 1.0
CA A:VAL65 4.4 22.5 1.0
OP2 D:DC3 4.5 21.1 1.0
CB A:VAL65 4.5 20.6 1.0
CD A:LYS60 4.7 22.1 1.0
O A:ALA59 4.7 19.6 1.0
CD A:PRO63 4.8 27.8 1.0
CB A:LEU62 4.8 21.8 1.0
O5' D:DC3 4.9 20.7 1.0
O3' D:DT2 4.9 17.9 1.0
CE A:LYS60 4.9 19.3 1.0
CB A:PRO63 5.0 26.0 1.0
N A:GLY66 5.0 22.9 1.0

Sodium binding site 3 out of 3 in 3isd

Go back to Sodium Binding Sites List in 3isd
Sodium binding site 3 out of 3 in the Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Human Dna Polymerase Beta with An Abasic Site (Thf): Dapcpp Mismatch within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na401

b:36.8
occ:1.00
O P:HOH184 2.5 32.2 1.0
N7 P:DG4 2.9 31.8 1.0
O P:HOH56 2.9 24.1 1.0
O6 P:DG4 3.8 25.9 1.0
C8 P:DG4 3.8 32.3 1.0
C5 P:DG4 3.9 29.1 1.0
C2' P:DT3 4.1 35.4 1.0
C6 P:DG4 4.2 27.9 1.0
N6 P:DA5 4.2 20.7 1.0

Reference:

W.A.Beard, D.D.Shock, V.K.Batra, L.C.Pedersen, S.H.Wilson. Dna Polymerase Beta Substrate Specificity: Side Chain Modulation of the "A-Rule". J.Biol.Chem. V. 284 31680 2009.
ISSN: ISSN 0021-9258
PubMed: 19759017
DOI: 10.1074/JBC.M109.029843
Page generated: Tue Dec 15 06:15:22 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy